251
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Kuan SL, Ng DYW, Wu Y, Förtsch C, Barth H, Doroshenko M, Koynov K, Meier C, Weil T. pH Responsive Janus-like Supramolecular Fusion Proteins for Functional Protein Delivery. J Am Chem Soc 2013; 135:17254-7. [DOI: 10.1021/ja4084122] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Seah Ling Kuan
- Institute
of Organic Chemistry III, Macromolecular Chemistry, University of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - David Y. W. Ng
- Institute
of Organic Chemistry III, Macromolecular Chemistry, University of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
- Max Planck Institute for Polymer Research Ackermannweg 10, D-55128 Mainz, Germany
| | - Yuzhou Wu
- Institute
of Organic Chemistry III, Macromolecular Chemistry, University of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
- Max Planck Institute for Polymer Research Ackermannweg 10, D-55128 Mainz, Germany
| | - Christina Förtsch
- Institute
of Pharmacology and Toxicology, University of Ulm Medical Center, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Holger Barth
- Institute
of Pharmacology and Toxicology, University of Ulm Medical Center, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Mikheil Doroshenko
- Max Planck Institute for Polymer Research Ackermannweg 10, D-55128 Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research Ackermannweg 10, D-55128 Mainz, Germany
| | - Christoph Meier
- Institute
of Organic Chemistry III, Macromolecular Chemistry, University of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - Tanja Weil
- Institute
of Organic Chemistry III, Macromolecular Chemistry, University of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
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252
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Božič S, Doles T, Gradišar H, Jerala R. New designed protein assemblies. Curr Opin Chem Biol 2013; 17:940-5. [PMID: 24183814 DOI: 10.1016/j.cbpa.2013.10.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 12/16/2022]
Abstract
Self-assembly is an essential concept of all organisms. Polypeptides self-assemble either within a single polypeptide chain or through assembly of protein domains. Recent advances in designed protein assemblies were achieved by genetic or chemical linkage of oligomerization domains and by engineering new interaction interfaces, which resulted in formation of lattices and cage-like protein assemblies. The absence of new experimentally determined protein folds in the last few years underlines the challenge of designing new folds. Recently a new strategy for designing self-assembly of a polypeptide fold, based on the topological arrangement of coiled-coil modules as the protein origami, has been proposed. The polypeptide tetrahedron was designed from a single chain concatenating of coiled-coil forming building modules interspersed with flexible hinges. In this strategy the order of coiled-coil segments defines the fold of the polypeptide nanostructure.
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Affiliation(s)
- Sabina Božič
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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253
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Fermani S, Falini G, Calvaresi M, Bottoni A, Calò V, Mangini V, Arnesano F, Natile G. Conformational Selection of Ubiquitin Quaternary Structures Driven by Zinc Ions. Chemistry 2013; 19:15480-4. [DOI: 10.1002/chem.201302229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Indexed: 02/06/2023]
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254
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Der BS, Kuhlman B. Strategies to control the binding mode of de novo designed protein interactions. Curr Opin Struct Biol 2013; 23:639-46. [PMID: 23731800 PMCID: PMC3737258 DOI: 10.1016/j.sbi.2013.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/19/2013] [Indexed: 12/14/2022]
Abstract
There has been significant recent progress in the computational design of protein interactions including the creation of novel heterodimers, homodimers, nanohedra, fibril caps and a protein crystal. Essential to these successes has been the use of innovative strategies for finding binding modes that are achievable, that is, identifying binding partners and docked conformations that can be successfully stabilized via sequence optimization and backbone refinement. In many cases this has involved the use of structural motifs commonly found at naturally occurring interfaces including alpha helices inserted into hydrophobic grooves, beta-strand pairing, metal binding, established helix packing motifs, and the use of symmetry to form cooperative interactions. Future challenges include the creation of hydrogen bond networks and antibody-like interactions based on the redesign of protein surface loops.
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Affiliation(s)
- Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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255
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Medina-Morales A, Perez A, Brodin JD, Tezcan FA. In vitro and cellular self-assembly of a Zn-binding protein cryptand via templated disulfide bonds. J Am Chem Soc 2013; 135:12013-22. [PMID: 23905754 DOI: 10.1021/ja405318d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Simultaneously strong and reversible through redox chemistry, disulfide bonds play a unique and often irreplaceable role in the formation of biological and synthetic assemblies. In an approach inspired by supramolecular chemistry, we report here that engineered noncovalent interactions on the surface of a monomeric protein can template its assembly into a unique cryptand-like protein complex ((C81/C96)RIDC14) by guiding the selective formation of multiple disulfide bonds across different interfaces. Owing to its highly interconnected framework, (C81/C96)RIDC14 is well preorganized for metal coordination in its interior, can support a large internal cavity surrounding the metal sites, and can withstand significant alterations in inner-sphere metal coordination. (C81/C96)RIDC14 self-assembles with high fidelity and yield in the periplasmic space of E. coli cells, where it can successfully compete for Zn(II) binding.
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Affiliation(s)
- Annette Medina-Morales
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356, USA
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256
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King NP, Lai YT. Practical approaches to designing novel protein assemblies. Curr Opin Struct Biol 2013; 23:632-8. [PMID: 23827813 DOI: 10.1016/j.sbi.2013.06.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/21/2013] [Accepted: 06/01/2013] [Indexed: 12/29/2022]
Abstract
Molecular self-assembly offers a means by which sophisticated materials can be constructed with unparalleled precision. Designing self-assembling protein structures is of particular interest as a result of the unique functional capabilities of proteins. Custom-designed protein materials could lead to new possibilities in therapeutics, bioenergy, and materials science. Although the field was long hampered by the challenges involved in designing such complex molecules, novel approaches and computational tools have recently led to remarkable progress. Here we review recent design studies in the context of three fundamental aspects of self-assembling materials: subunit organization, subunit interactions, and regulation of assembly.
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Affiliation(s)
- Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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257
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Shin SH, Comolli LR, Tscheliessnig R, Wang C, Nam KT, Hexemer A, Siegerist CE, De Yoreo JJ, Bertozzi CR. Self-assembly of "S-bilayers", a step toward expanding the dimensionality of S-layer assemblies. ACS NANO 2013; 7:4946-4953. [PMID: 23705800 DOI: 10.1021/nn400263j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein-based assemblies with ordered nanometer-scale features in three dimensions are of interest as functional nanomaterials but are difficult to generate. Here we report that a truncated S-layer protein assembles into stable bilayers, which we characterized using cryogenic-electron microscopy, tomography, and X-ray spectroscopy. We find that emergence of this supermolecular architecture is the outcome of hierarchical processes; the proteins condense in solution to form 2-D crystals, which then stack parallel to one another to create isotropic bilayered assemblies. Within this bilayered structure, registry between lattices in two layers was disclosed, whereas the intrinsic symmetry in each layer was altered. Comparison of these data to images of wild-type SbpA layers on intact cells gave insight into the interactions responsible for bilayer formation. These results establish a platform for engineering S-layer assemblies with 3-D architecture.
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Affiliation(s)
- Seong-Ho Shin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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258
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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259
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Lai YT, Tsai KL, Sawaya MR, Asturias FJ, Yeates TO. Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly. J Am Chem Soc 2013; 135:7738-43. [PMID: 23621606 DOI: 10.1021/ja402277f] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Designing protein molecules that self-assemble into complex architectures is an outstanding goal in the area of nanobiotechnology. One design strategy for doing this involves genetically fusing together two natural proteins, each of which is known to form a simple oligomer on its own (e.g., a dimer or trimer). If two such components can be fused in a geometrically predefined configuration, that designed subunit can, in principle, assemble into highly symmetric architectures. Initial experiments showed that a 12-subunit tetrahedral cage, 16 nm in diameter, could be constructed following such a procedure [Padilla, J. E.; et al. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2217; Lai, Y. T.; et al. Science 2012, 336, 1129]. Here we characterize multiple crystal structures of protein cages constructed in this way, including cages assembled from two mutant forms of the same basic protein subunit. The flexibilities of the designed assemblies and their deviations from the target model are described, along with implications for further design developments.
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Affiliation(s)
- Yen-Ting Lai
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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260
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Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nat Chem Biol 2013; 9:362-6. [PMID: 23624438 PMCID: PMC3661711 DOI: 10.1038/nchembio.1248] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/28/2013] [Indexed: 01/30/2023]
Abstract
Protein structures evolved through a complex interplay of cooperative interactions and it is still very challenging to design new protein folds de novo. Here, we present a strategy to design self-assembling polypeptide nanostructured polyhedra, based on modularization using orthogonal dimerizing segments. We designed end experimentally demonstrated formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled-coil-forming segments separated by flexible peptide hinges. Path of the polypeptide chain is guided by the defined order of segments that traverse each of the 6 edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. Coincidence of the polypeptide termini in the same vertex is demonstrated by reconstitution of the split fluorescent protein by the polypeptide with the correct tetrahedral topology, while polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides the basis for construction of new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.
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261
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Marsh J, Hernández H, Hall Z, Ahnert S, Perica T, Robinson C, Teichmann S. Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell 2013; 153:461-70. [PMID: 23582331 PMCID: PMC4009401 DOI: 10.1016/j.cell.2013.02.044] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/05/2013] [Accepted: 02/21/2013] [Indexed: 01/13/2023]
Abstract
Is the order in which proteins assemble into complexes important for biological function? Here, we seek to address this by searching for evidence of evolutionary selection for ordered protein complex assembly. First, we experimentally characterize the assembly pathways of several heteromeric complexes and show that they can be simply predicted from their three-dimensional structures. Then, by mapping gene fusion events identified from fully sequenced genomes onto protein complex assembly pathways, we demonstrate evolutionary selection for conservation of assembly order. Furthermore, using structural and high-throughput interaction data, we show that fusion tends to optimize assembly by simplifying protein complex topologies. Finally, we observe protein structural constraints on the gene order of fusion that impact the potential for fusion to affect assembly. Together, these results reveal the intimate relationships among protein assembly, quaternary structure, and evolution and demonstrate on a genome-wide scale the biological importance of ordered assembly pathways.
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Affiliation(s)
- Joseph A. Marsh
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helena Hernández
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Zoe Hall
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Sebastian E. Ahnert
- Theory of Condensed Matter, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Tina Perica
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Sarah A. Teichmann
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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262
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Doll TAPF, Raman S, Dey R, Burkhard P. Nanoscale assemblies and their biomedical applications. J R Soc Interface 2013; 10:20120740. [PMID: 23303217 DOI: 10.1098/rsif.2012.0740] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nanoscale assemblies are a unique class of materials, which can be synthesized from inorganic, polymeric or biological building blocks. The multitude of applications of this class of materials ranges from solar and electrical to uses in food, cosmetics and medicine. In this review, we initially highlight characteristic features of polymeric nanoscale assemblies as well as those built from biological units (lipids, nucleic acids and proteins). We give special consideration to protein nanoassemblies found in nature such as ferritin protein cages, bacterial microcompartments and vaults found in eukaryotic cells and designed protein nanoassemblies, such as peptide nanofibres and peptide nanotubes. Next, we focus on biomedical applications of these nanoscale assemblies, such as cell targeting, drug delivery, bioimaging and vaccine development. In the vaccine development section, we report in more detail the use of virus-like particles and self-assembling polypeptide nanoparticles as new vaccine delivery platforms.
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Affiliation(s)
- Tais A P F Doll
- Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269, USA
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263
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Ardejani MS, Chok XL, Foo CJ, Orner BP. Complete shift of ferritin oligomerization toward nanocage assembly via engineered protein–protein interactions. Chem Commun (Camb) 2013; 49:3528-30. [DOI: 10.1039/c3cc40886h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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264
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Abstract
Protein nanotechnology is an emerging field that is still defining itself. It embraces the intersection of protein science, which exists naturally at the nanoscale, and the burgeoning field of nanotechnology. In this opening chapter, a select review is given of some of the exciting nanostructures that have already been created using proteins, and the sorts of applications that protein engineers are reaching towards in the nanotechnology space. This provides an introduction to the rest of the volume, which provides inspirational case studies, along with tips and tools to manipulate proteins into new forms and architectures, beyond Nature's original intentions.
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Affiliation(s)
- Juliet A Gerrard
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, MacDiarmid Institute for Advanced Materials and Nanotechnology, Riddet Institute, Christchurch, New Zealand
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265
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Sanghamitra NJM, Ueno T. Expanding coordination chemistry from protein to protein assembly. Chem Commun (Camb) 2013; 49:4114-26. [DOI: 10.1039/c2cc36935d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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266
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Engineering protein filaments with enhanced thermostability for nanomaterials. Biotechnol J 2012; 8:228-36. [DOI: 10.1002/biot.201200009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/07/2012] [Accepted: 08/30/2012] [Indexed: 11/07/2022]
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267
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Oohora K, Onoda A, Hayashi T. Supramolecular assembling systems formed by heme-heme pocket interactions in hemoproteins. Chem Commun (Camb) 2012; 48:11714-26. [PMID: 23079761 DOI: 10.1039/c2cc36376c] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A native protein in a biological system spontaneously produces large and elegant assemblies via self-assembly or assembly with various biomolecules which provide non-covalent interactions. In this context, the protein plays a key role in construction of a unique supramolecular structure operating as a functional system. Our group has recently highlighted the structure and function of hemoproteins reconstituted with artificially created heme analogs. The heme molecule is a replaceable cofactor of several hemoproteins. Here, we focus on the successive supramolecular protein assemblies driven by heme-heme pocket interactions to afford various examples of protein fibers, networks and three-dimensional clusters in which an artificial heme moiety is introduced onto the surface of a hemoprotein via covalent linkage and the native heme cofactor is removed from the heme pocket. This strategy is found to be useful for constructing hybrid materials with an electrode or with nanoparticles. The new systems described herein are expected to lead to the generation of various biomaterials with functions and characteristic physicochemical properties similar to those of hemoproteins.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
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268
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Modica JA, Skarpathiotis S, Mrksich M. Modular assembly of protein building blocks to create precisely defined megamolecules. Chembiochem 2012; 13:2331-4. [PMID: 23070998 PMCID: PMC3804166 DOI: 10.1002/cbic.201200501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 11/10/2022]
Abstract
Enzyme-promoted assembly: The construction of a hetero-bifunctional protein building block, HaloTag-cutinase, that reacts rapidly and selectively with a small-molecule linker is described. The step-wise combination of these building blocks generates a 300 kDa "megamolecule" with precisely defined domain orientation, connectivity, and composition.
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Affiliation(s)
- Justin A Modica
- Departments of Chemistry and Biomedical Engineering, Howard Hughes Medical Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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269
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Abstract
Proteins are the work-horses of life and excute the essential processes involved in the growth and repair of cells. These roles include all aspects of cell signalling, metabolism and repair that allow living things to exist. They are not only chemical catalysts and machine components, they are also structural components of the cell or organism, capable of self-organisation into strong supramolecular cages, fibres and meshes. How proteins are encoded genetically and how they are sythesised in vivo is now well understood, and for an increasing number of proteins, the relationship between structure and function is known in exquisite detail. The next challenge in bionanoscience is to adapt useful protein systems to build new functional structures. Well-defined natural structures with potential useful shapes are a good starting point. With this in mind, in this chapter we discuss the properties of natural and artificial protein channels, nanotubes and cages with regard to recent progress and potential future applications. Chemistries for attaching together different proteins to form superstructures are considered as well as the difficulties associated with designing complex protein structures ab initio.
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Affiliation(s)
- Jonathan G. Heddle
- Heddle Initiative Research Unit RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Jeremy R. H. Tame
- Protein Design Laboratory Yokohama City University 1-7—29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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270
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Zhang W, Luo Q, Miao L, Hou C, Bai Y, Dong Z, Xu J, Liu J. Self-assembly of glutathione S-transferase into nanowires. NANOSCALE 2012; 4:5847-5851. [PMID: 22907071 DOI: 10.1039/c2nr31244a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study presents the Ni-ion-directed self-assembly of a C(2)-symmetric homodimeric enzyme into nanowires. A genetically introduced His-tag arm stretches out of the central structure of a C(2)-symmetric homodimer of glutathione S-transferase, which is used as a linker to recruit a second building block through interprotein metal coordination, forming self-assembled one-dimensional nanostructures with excellent enzymatic activity.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Road, Changchun 130012, China
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271
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Lai YT, King NP, Yeates TO. Principles for designing ordered protein assemblies. Trends Cell Biol 2012; 22:653-61. [PMID: 22975357 DOI: 10.1016/j.tcb.2012.08.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/10/2012] [Accepted: 08/12/2012] [Indexed: 11/18/2022]
Abstract
In nature, many proteins have evolved to have self-complementary shapes. This drives them to assemble into supramolecular structures, sometimes of great complexity, and often carrying out sophisticated cellular functions. Designing novel proteins that can self-assemble into similarly complex structures is a longstanding goal in bioengineering. New ideas, combined with continually improving computer algorithms, are making it possible to advance on that goal, bringing wide-ranging applications in synthetic biology within reach. Prospective applications range from vaccine design to molecular delivery to bioactive materials. Recent strategies and examples of successfully designed protein cages, layers, and crystals are reviewed.
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Affiliation(s)
- Yen-Ting Lai
- Biomedical Engineering Interdepartmental Degree Program, University of California, Los Angeles, CA, USA
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272
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Boyle AL, Bromley EHC, Bartlett GJ, Sessions RB, Sharp TH, Williams CL, Curmi PMG, Forde NR, Linke H, Woolfson DN. Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design. J Am Chem Soc 2012; 134:15457-67. [PMID: 22917063 DOI: 10.1021/ja3053943] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design of bioinspired nanostructures and materials of defined size and shape is challenging as it pushes our understanding of biomolecular assembly to its limits. In such endeavors, DNA is the current building block of choice because of its predictable and programmable self-assembly. The use of peptide- and protein-based systems, however, has potential advantages due to their more-varied chemistries, structures and functions, and the prospects for recombinant production through gene synthesis and expression. Here, we present the design and characterization of two complementary peptides programmed to form a parallel heterodimeric coiled coil, which we use as the building blocks for larger, supramolecular assemblies. To achieve the latter, the two peptides are joined via peptidic linkers of variable lengths to produce a range of assemblies, from flexible fibers of indefinite length, through large colloidal-scale assemblies, down to closed and discrete nanoscale objects of defined stoichiometry. We posit that the different modes of assembly reflect the interplay between steric constraints imposed by short linkers and the bulk of the helices, and entropic factors that favor the formation of many smaller objects as the linker length is increased. This approach, and the resulting linear and proteinogenic polypeptides, represents a new route for constructing complex peptide-based assemblies and biomaterials.
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Affiliation(s)
- Aimee L Boyle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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273
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Abstract
Bionanotechnology seeks to modify and design new biopolymers and their applications and uses biological systems as cell factories for the production of nanomaterials. Molecular self-assembly as the main organizing principle of biological systems is also the driving force for the assembly of artificial bionanomaterials. Protein domains and peptides are particularly attractive as building blocks because of their ability to form complex three-dimensional assemblies from a combination of at least two oligomerization domains that have the oligomerization state of at least two and three respectively. In the present paper, we review the application of polypeptide-based material for the formation of material with nanometre-scale pores that can be used for the separation. Use of antiparallel coiled-coil dimerization domains introduces the possibility of modulation of pore size and chemical properties. Assembly or disassembly of bionanomaterials can be regulated by an external signal as demonstrated by the coumermycin-induced dimerization of the gyrase B domain which triggers the formation of polypeptide assembly.
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274
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White BR, Carlson JCT, Kerns JL, Wagner CR. Protein interface remodeling in a chemically induced protein dimer. J Mol Recognit 2012; 25:393-403. [DOI: 10.1002/jmr.2196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brian R. White
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jonathan C. T. Carlson
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jessie L. Kerns
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Carston R. Wagner
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
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275
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King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 2012; 336:1171-4. [PMID: 22654060 PMCID: PMC4138882 DOI: 10.1126/science.1219364] [Citation(s) in RCA: 488] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
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Affiliation(s)
- Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Breanna S. Vollmar
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John P. Sumida
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98177, USA
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tamir Gonen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Todd O. Yeates
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA 90095, USA,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA,To whom correspondence should be addressed.
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276
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Lai YT, Cascio D, Yeates TO. Structure of a 16-nm Cage Designed by Using Protein Oligomers. Science 2012; 336:1129. [DOI: 10.1126/science.1219351] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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277
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Chen HN, Woycechowsky KJ. Conversion of a dodecahedral protein capsid into pentamers via minimal point mutations. Biochemistry 2012; 51:4704-12. [PMID: 22606973 DOI: 10.1021/bi3003555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein self-assembly relies upon the formation of stabilizing noncovalent interactions across subunit interfaces. Identifying the determinants of self-assembly is crucial for understanding structure-function relationships in symmetric protein complexes and for engineering responsive nanoscale architectures for applications in medicine and biotechnology. Lumazine synthases (LS's) comprise a protein family that forms diverse quaternary structures, including pentamers and 60-subunit dodecahedral capsids. To improve our understanding of the basis for this difference in assembly, we attempted to convert the capsid-forming LS from Aquifex aeolicus (AaLS) into pentamers through a small number of rationally designed amino acid substitutions. Our mutations targeted side chains at ionic (R40), hydrogen bonding (H41), and hydrophobic (L121 and I125) interaction sites along the interfaces between pentamers. We found that substitutions at two or three of these positions could reliably generate pentameric variants of AaLS. Biophysical characterization indicates that this quaternary structure change is not accompanied by substantial changes in secondary or tertiary structure. Interestingly, previous homology-based studies of the assembly determinants in LS's had identified only one of these four positions. The ability to control assembly state in protein capsids such as AaLS could aid efforts in the development of new systems for drug delivery, biocatalysis, or materials synthesis.
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Affiliation(s)
- Hsiao-Nung Chen
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
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278
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Randolph LM, Chien MP, Gianneschi NC. Biological stimuli and biomolecules in the assembly and manipulation of nanoscale polymeric particles. Chem Sci 2012; 3:10.1039/C2SC00857B. [PMID: 24353895 PMCID: PMC3864871 DOI: 10.1039/c2sc00857b] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Living systems are replete with complex, stimuli-responsive nanoscale materials and molecular self-assemblies. There is an ever increasing and intense interest within the chemical sciences to understand, mimic and interface with these biological systems utilizing synthetic and/or semi-synthetic tools. Our aim in this review is to give perspective on this emerging field of research by highlighting examples of polymeric nanoparticles and micelles that are prepared utilizing biopolymers together with synthetic polymers for the purpose of developing nanomaterials capable of interacting and responding to biologically relevant stimuli. It is expected that with the merging of evolved biological molecules with synthetic materials, will come the ability to prepare complex, functional devices. A variety of applications will become accessible including self-healing materials, self-replicating systems, biodiagnostic tools, drug targeting materials and autonomous, adaptive sensors. Most importantly, the success of this type of strategy will impact how biomolecules are stabilized and incorporated into synthetic devices and at the same time, will influence how synthetic materials are utilized within biomedical applications.
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Affiliation(s)
| | | | - Nathan C. Gianneschi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
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279
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Abstract
Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.
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280
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281
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282
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Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat Chem 2012; 4:375-82. [PMID: 22522257 PMCID: PMC3335442 DOI: 10.1038/nchem.1290] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 02/01/2012] [Indexed: 12/12/2022]
Abstract
Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH.
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283
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Ghosh P, Mushtaq AU, Durani S. Computational design by evolving folds and assemblies over the alphabet in l- and d-α-amino acids. RSC Adv 2012. [DOI: 10.1039/c2ra01012g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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284
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Staples JK, Oshaben KM, Horne WS. A modular synthetic platform for the construction of protein-based supramolecular polymers via coiled-coil self-assembly. Chem Sci 2012. [DOI: 10.1039/c2sc20729j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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285
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Abstract
Although people taking different approaches in the field of nanotechnology may target different size ranges, broadly, nanotechnology has the goal of creating structures in the 1-100 nm size range. This is the same size range that bacteriophages synthesize capsids. Bacteriophages also have the desirable property of self-fabrication or self-assembly--much of capsid structural assembly information is a function of the capsid proteins themselves rather than requiring other proteins. This would seem to make bacteriophage protein-based materials ideal for some nanotechnology applications. So far, the majority of research has taken one of two approaches: first, using filamentous bacteriophage display techniques to identify inorganic nanocrystal-binding peptides and using those peptides and the filamentous phage virions to create novel materials, and second, using a variety of bacteriophage and bacteriophage receptor-binding proteins to functionalize surfaces to create biosensors for bacterial detection. Here, I review these two approaches and speculate on some of the challenges for further development of bacteriophage protein-based self-assembling nanomaterials.
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286
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Nakanishi T, Naito M, Takeoka Y, Matsuura K. Versatile self-assembled hybrid systems with exotic structures and unique functions. Curr Opin Colloid Interface Sci 2011. [DOI: 10.1016/j.cocis.2011.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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287
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Optimizing the refolding conditions of self-assembling polypeptide nanoparticles that serve as repetitive antigen display systems. J Struct Biol 2011; 177:168-76. [PMID: 22115997 PMCID: PMC7118850 DOI: 10.1016/j.jsb.2011.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/18/2022]
Abstract
Nanoparticles show great promise as potent vaccine candidates since they are readily taken up by the antigen presenting cells of the immune system. The particle size and the density of the B cell epitopes on the surface of the particles greatly influences the strength of the humoral immune response. We have developed a novel type of nanoparticle composed of peptide building blocks (Raman et al., 2006) and have used such particles to design vaccines against malaria and SARS (Kaba et al., 2009, Pimentel et al., 2009). Here we investigate the biophysical properties and the refolding conditions of a prototype of these self-assembling polypeptide nanoparticles (SAPNs). SAPNs are formed from a peptide containing a pentameric and a trimeric coiled-coil domain. At near physiological conditions the peptide self-assembles into about 27 nm, roughly spherical SAPNs. The average size of the SAPNs increases with the salt concentration. The optimal pH for their formation is between 7.5 and 8.5, while aggregation occurs at lower and higher values. A glycerol concentration of about 5% v/v is required for the formation of SAPNs with regular spherical shapes. These studies will help to optimize the immunological properties of SAPNs.
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288
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Patterson DP, Desai AM, Holl MMB, Marsh ENG. Evaluation of a symmetry-based strategy for assembling protein complexes. RSC Adv 2011; 1:1004-1012. [PMID: 23293744 PMCID: PMC3536532 DOI: 10.1039/c1ra00282a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We evaluate a strategy for assembling proteins into large cage-like structures, based on the symmetry associated with the native protein's quaternary structure. Using a trimeric protein, KDPG aldolase, as a building block, two fusion proteins were designed that could assemble together upon mixing. The fusion proteins, designated A-(+) and A-(-), comprise the aldolase domain, a short, flexible spacer sequence, and a sequence designed to form a heterodimeric antiparallel coiled-coil between A-(+) and A-(-). The flexible spacer is included to minimize constraints on the ability of the fusion proteins to assemble into larger structures. On incubating together, A-(+) and A-(-) assembled into a mixture of complexes that were analyzed by size exclusion chromatography coupled to multi-angle laser light scattering, analytical ultracentrifugation, transmission electron microscopy and atomic force microscopy. Our analysis indicates that, despite the inherent flexibility of the assembly strategy, the proteins assemble into a limited number of globular structures. Dimeric and tetrameric complexes of A-(+) and A-(-) predominate, with some evidence for the formation of larger assemblies; e.g. octameric A-(+): A-(-) complexes.
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Affiliation(s)
| | - Ankur M. Desai
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark M. Banaszak Holl
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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289
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Zhang Y, Orner BP. Self-assembly in the ferritin nano-cage protein superfamily. Int J Mol Sci 2011; 12:5406-21. [PMID: 21954367 PMCID: PMC3179174 DOI: 10.3390/ijms12085406] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 08/09/2011] [Accepted: 08/15/2011] [Indexed: 11/17/2022] Open
Abstract
Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.
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Affiliation(s)
- Yu Zhang
- Division of Chemistry and Biology Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore; E-Mail:
| | - Brendan P. Orner
- Division of Chemistry and Biology Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore; E-Mail:
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290
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291
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Sinclair JC, Davies KM, Vénien-Bryan C, Noble MEM. Generation of protein lattices by fusing proteins with matching rotational symmetry. NATURE NANOTECHNOLOGY 2011; 6:558-62. [PMID: 21804552 DOI: 10.1038/nnano.2011.122] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/29/2011] [Indexed: 05/15/2023]
Abstract
The self-assembly of supramolecular structures that are ordered on the nanometre scale is a key objective in nanotechnology. DNA and peptide nanotechnologies have produced various two- and three-dimensional structures, but protein molecules have been underexploited in this area of research. Here we show that the genetic fusion of subunits from protein assemblies that have matching rotational symmetry generates species that can self-assemble into well-ordered, pre-determined one- and two-dimensional arrays that are stabilized by extensive intermolecular interactions. This new class of supramolecular structure provides a way to manufacture biomaterials with diverse structural and functional properties.
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Affiliation(s)
- John C Sinclair
- Laboratory of Molecular Biophysics, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK.
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292
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Howorka S. Rationally engineering natural protein assemblies in nanobiotechnology. Curr Opin Biotechnol 2011; 22:485-91. [PMID: 21664809 DOI: 10.1016/j.copbio.2011.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 01/07/2023]
Abstract
Multimeric protein assemblies are essential components in viruses, bacteria, eukaryotic cells, and organisms where they act as cytoskeletal scaffold, storage containers, or for directional transport. The bottom-up structures can be exploited in nanobiotechnology by harnessing their built-in properties and combining them with new functional modules. This review summarizes the design principles of natural protein assemblies, highlights recent progress in their structural elucidation, and shows how rational engineering can create new biomaterials for applications in vaccine development, biocatalysis, materials science, and synthetic biology.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
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293
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Ku TH, Chien MP, Thompson MP, Sinkovits RS, Olson NH, Baker TS, Gianneschi NC. Controlling and switching the morphology of micellar nanoparticles with enzymes. J Am Chem Soc 2011; 133:8392-5. [PMID: 21462979 PMCID: PMC3756928 DOI: 10.1021/ja2004736] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Micelles were prepared from polymer-peptide block copolymer amphiphiles containing substrates for protein kinase A, protein phosphatase-1, and matrix metalloproteinases 2 and 9. We examine reversible switching of the morphology of these micelles through a phosphorylation-dephosphorylation cycle and study peptide-sequence directed changes in morphology in response to proteolysis. Furthermore, the exceptional uniformity of these polymer-peptide particles makes them amenable to cryo-TEM reconstruction techniques lending insight into their internal structure.
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Affiliation(s)
- Ti-Hsuan Ku
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Miao-Ping Chien
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Matthew P. Thompson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Robert S. Sinkovits
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Norman H. Olson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Timothy S. Baker
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Nathan C. Gianneschi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
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294
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Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. Protein Pept Lett 2011; 18:362-72. [PMID: 21222638 PMCID: PMC7316382 DOI: 10.2174/092986611794653996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 12/15/2010] [Indexed: 11/22/2022]
Abstract
We construct nanotubes using native protein structures and their native associations from structural databases. The construction is based on a shape-guided symmetric self-assembly concept. Our strategy involves fusing judiciously-selected oligomerization domains via peptide linkers. Linkers are inherently flexible, hence their choice is critical: they should position the domains in three-dimensional space in the desired orientation while retaining their own natural conformational tendencies; however, at the same time, retain the construct stability. Here we outline a design scheme which accounts for linker flexibility considerations, and present two examples. The first is HIV-1 capsid protein, which in vitro self-assembles into nanotubes and conical capsids, and its linker exists as a short flexible loop. The second involves novel nanotubes construction based on antimicrobial homodimer Magainin 2, employing linkers of distinct lengths and flexibility levels. Our strategy utilizes the abundance of unique shapes and sizes of proteins and their building blocks which can assemble into a vast number of combinations, and consequently, nanotubes of distinct morphologies and diameters. Computational design and assessment methodologies can help reduce the number of candidates for experimental validation. This is an invited paper for a special issue on protein dynamics, here focusing on flexibility in nanotube design based on protein building blocks.
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Affiliation(s)
- Idit Buch
- Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI – Frederick, Bldg 469, Frederick, MD 21702, USA
| | - Haim J. Wolfson
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Nussinov
- Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI – Frederick, Bldg 469, Frederick, MD 21702, USA
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295
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Matsuura K, Watanabe K, Matsuzaki T, Sakurai K, Kimizuka N. Self-assembled synthetic viral capsids from a 24-mer viral peptide fragment. Angew Chem Int Ed Engl 2011; 49:9662-5. [PMID: 21077072 DOI: 10.1002/anie.201004606] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
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296
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Jutz G, Böker A. Bionanoparticles as functional macromolecular building blocks – A new class of nanomaterials. POLYMER 2011. [DOI: 10.1016/j.polymer.2010.11.047] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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297
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Mori Y, Minamihata K, Abe H, Goto M, Kamiya N. Protein assemblies by site-specific avidin–biotin interactions. Org Biomol Chem 2011; 9:5641-4. [DOI: 10.1039/c1ob05428g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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298
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Müller MK, Petkau K, Brunsveld L. Proteinassembly along a supramolecular wire. Chem Commun (Camb) 2011; 47:310-2. [DOI: 10.1039/c0cc02084b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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299
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Lamarre B, Ryadnov MG. Self-assembling viral mimetics: one long journey with short steps. Macromol Biosci 2010; 11:503-13. [PMID: 21165940 DOI: 10.1002/mabi.201000330] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Indexed: 12/14/2022]
Abstract
Recently, the Foresight Institute has pronounced six economic challenges that can be addressed through the progress of nanotechnology. One of these is the health and longevity of human life. Amongst applications anticipated to provide a solution to this challenge, gene therapy appears to be particularly promising. In theory, many diseases that result from genetic disorders can be cured by correcting defective genes. In practice, finding efficient and safe delivery vectors remains the stumbling point on the path of genetic therapies to the clinic. Viruses, otherwise the most efficient transfectors, pose safety concerns over immune reactions, whereas synthetic gene packages greatly lack the structural integrity of viruses. An ideal vector is therefore seen as a compromise between the two: a nanoscale device, which would mimic a virus and act as a virus, but would do this at the designer's whim. A strategy to achieve this is offered by the virus architecture itself, the principles of which are translated into the function via exquisitely reproducible self-assembly mechanisms. Thus, to mimic a virus is to mimic the way it is built, i.e., self-assembly. With just a few attempts made so far, the journey to an artificial virus has had a short lifetime, but the promise it holds is not expected to reduce any time soon.
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Affiliation(s)
- Baptiste Lamarre
- National Physical Laboratory, Teddington, Middlesex, TW110LW, UK
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300
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Matsuura K, Watanabe K, Matsuzaki T, Sakurai K, Kimizuka N. Self-Assembled Synthetic Viral Capsids from a 24-mer Viral Peptide Fragment. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004606] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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